Class SinglePassSamProgram

    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="Input SAM/BAM/CRAM file.")
        public File INPUT
      • OUTPUT

        protected File OUTPUT
      • ASSUME_SORTED

        @Argument(doc="If true (default), then the sort order in the header file will be ignored.",
                  shortName="AS")
        public boolean ASSUME_SORTED
      • STOP_AFTER

        @Argument(doc="Stop after processing N reads, mainly for debugging.")
        public long STOP_AFTER
    • Constructor Detail

      • SinglePassSamProgram

        public SinglePassSamProgram()
    • Method Detail

      • setReferenceSequence

        public void setReferenceSequence​(File referenceFile)
        Set the reference File.
      • doWork

        protected final int doWork()
        Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.
        Specified by:
        doWork in class CommandLineProgram
        Returns:
        program exit status.
      • usesNoRefReads

        protected boolean usesNoRefReads()
        Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.
      • setup

        protected abstract void setup​(htsjdk.samtools.SAMFileHeader header,
                                      File samFile)
        Should be implemented by subclasses to do one-time initialization work.
      • acceptRead

        protected abstract void acceptRead​(htsjdk.samtools.SAMRecord rec,
                                           htsjdk.samtools.reference.ReferenceSequence ref)
        Should be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.
      • finish

        protected abstract void finish()
        Should be implemented by subclasses to do one-time finalization work.